[Bioperl-l] results problem with StandAloneBlast

[Sendu Bala]

Genevieve DeClerck wrote:
> Thanks for your comment Sendu, it was very helpful. I think this must be 
> what's going on.. I am using $blast_report->next_result in both 
> subroutines. It appears that analyzing the blast results first w/ my 
> sort subroutine empties (?) the $blast_result object so that when I try 
> to print, there is nothing left to print. (and visa-versa when I print 
> first then try to sort).
> So, from the looks of things, using next_result has the effect of 
> popping the Bio::Search::Result::ResultI objects off of the SearchIO 
> blast report object??

Not quite. It's more or less exactly like opening a file and then trying 
to read it all twice like this:
open(FILE, "file");
while (<FILE>) {
     print # prints each line in the file
}
while (<FILE>) {
     print # never happens, we never enter this while loop
}

To get the second while loop to print anything we need to say seek(FILE, 
0, 0) before it. Or in the first while loop store each line in an array, 
and then make the second loop a foreach through that array.


> It seems I could get around this by making a copy of the blast report by 
> setting it to another new variable...(not the most elegant solution) but 
> I'm having trouble with this...
> 
> If I do:
> 
>     my $blast_report_copy = $blast_report;
> 
> I'm just copying the reference to the SearchIO blast result, so it 
> doesn't help me. How can I make another physical copy of this blast 
> result object? Seems like a simple thing but how to do it is escaping me.

Not really a good idea, and it may not work anyway if the object 
contains a filehandle. But for a simple object you might recursively 
loop through the data structure and copy each element out into a similar 
data structure.


> But better yet, the way to go is to 'reset the counter,' or to find a 
> way to look at/print/sort the results without removing data from the 
> blast result object. How is this done though??

It would be rather nice if this worked:
my $blast_report = $factory->blastall($ref_seq_objs);
my $blast_fh = $blast_report->fh();
while (<$blast_fh>) {
     # $_ is a ResultI object, use as normal
}
seek($blast_fh, 0, 0); # this would be great, but does it work?
while <$blast_fh>) {
     # go through the results again in your second subroutine
}

An alternative hacky way of doing it, which may also not work, would be 
to go through your $blast_report as normal, but then before going 
through it a second time, say
my $fh = $blast_report->_fh;
seek($fh, 0, 0);

Finally, the most sensible way (assuming bioperl provides no methods of 
its own for this) of solving the problem is, the first time you go 
through each next_result, next_hit and next_hsp, just store the returned 
objects in an array of arrays of arrays. Then the second time get the 
objects from your array structure instead of with the method calls.